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Related Concept Videos

The Nucleosome01:19

The Nucleosome

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Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...
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Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
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Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
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Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
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Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
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Related Experiment Video

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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
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Hi-CO: 3D genome structure analysis with nucleosome resolution.

Masae Ohno1,2, Tadashi Ando3,4, David G Priest1,5

  • 1Laboratory for Cell Systems Control, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan.

Nature Protocols
|May 29, 2021
PubMed
Summary
This summary is machine-generated.

We developed high-throughput chromosome conformation capture with nucleosome orientation (Hi-CO) technology to map 3D nucleosome positions and orientations. This method reveals genome organization at the nucleosome level for a deeper understanding of genome function.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Biophysics

Background:

  • Nucleosomes are fundamental genome organizational units.
  • Nucleosome folding impacts genome functions and protein interactions.
  • Existing methods lack nucleosome-level 3D spatial resolution.

Purpose of the Study:

  • To introduce high-throughput chromosome conformation capture with nucleosome orientation (Hi-CO) technology.
  • To enable 3D mapping of nucleosome positions and orientations genome-wide.
  • To provide high-resolution insights into genome organization.

Main Methods:

  • Developed an improved high-throughput chromosome conformation capture (Hi-C) experimental procedure for nucleosome proximity analysis.
  • Utilized micrococcal nuclease digestion and ligation of DNA entry/exit points.
  • Employed simulated annealing-molecular dynamics for computational 3D modeling.

Main Results:

  • Achieved proximity analysis at individual nucleosome loci, surpassing conventional Hi-C resolution.
  • Successfully excluded unwanted ligation products for cleaner data.
  • Mapped 66,360 nucleosome loci in Saccharomyces cerevisiae at 6.8 nm resolution.

Conclusions:

  • Hi-CO technology provides unprecedented 3D resolution of nucleosome organization.
  • This advancement facilitates detailed studies of genome folding and function.
  • The technique offers a powerful new tool for chromatin biology research.